modeller_usage

modeller_usage@salilab.org

4 participants
3146 discussions

Close contacts between protein and ligand
by majort＠biu.ac.il 21 Jul '23

21 Jul '23

Hi I'm modeling protein with ligands (using the "." options in the sequence file). However, in the final models the contacts between protein side chains and ligands are too close (the template and target have differently sized ligands; the template target ligand has a smaller ligand). Is there a way to avoid this, like giving less weight to the homology terms and greater weight to the standard FF terms? Thanks, Dan

2 1

Adding loops to X-Ray
by majort＠biu.ac.il 16 Jun '23

16 Jun '23

Hi, I'm trying to add 3 loops to a crystal structure (loops are missing) without making any changes to the original X-Ray. I base the script on the existing example script 'examples/automodel/loop.py'. My script: ########################################################## from modeller import * from modeller.automodel import * # Load the AutoModel class log.verbose() env = Environ() code = '5uv1' # directories for input atom files env.io.atom_files_directory = ['.'] # Override the regular LoopModel class to select our own loops class MyLoop(LoopModel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # Select gaps for loop modeling return Selection(self.residue_range('157:A', '163:A'), self.residue_range('434:A', '439:A'), self.residue_range('507:A', '517:A')) a = MyLoop(env, inimodel='5uv1_fill.B99990001.pdb', #code+'.pdb', # initial model of the target sequence=code, # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE a.loop.starting_model = 1 # First loop model a.loop.ending_model = 4 # Last loop model a.loop.md_level = refine.very_fast # Loop model refinement level a.make() ########################################################## In the inimodel ('5uv1_fill.B99990001.pdb'), the missing residues have been added and simply appear as a straight line and are only connected to one end. When I try do loop modeling using the above script, the loop atoms hardly move and don't reconnect to the other endpoint. How can I model the loops without making any change to the other atoms. Thanks, Dan

2 3

Negative molpdf values
by Isabel Elliott 23 Mar '23

23 Mar '23

Hi, I am generating and refining models using the LoopModel or DOPELoopModel or DOPEHRLoopModel methods. Sometimes I get negative molpdf values for some of my generated models. What does this mean? I thought that the molpdf should be positive. The models with the most negative molpdf correspond to the most negative (i.e the lowest) DOPE scores - are these therefore the best models? Thanks.

2 1

Design of a chmieric protein from two known structures
by dafnikarr＠gmail.com 15 Mar '23

15 Mar '23

Hello , i want to design a chimeric protein by fusion of subdomains of two known proteins. Do you know how should write the relevant scripts? And how to do the alignment? Should i use the multi template approach and use the two proteins as a template? Thank you! Dafni

3 2

MODELLER installation
by Sehrish Batool 28 Feb '23

28 Feb '23

Hello, I hope this email finds you well. I am struggling to download MODELLER application but facing certian security issues. Can you please help me and guide how can I download and install it. I need Modeller to run a workshop in school to show students the advancement in scientific studies. Thank you. J Kind regards:Sehrish Sent from Yahoo Mail on Android

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Modeller is transforming ZN2 atom names to ZN
by Pedro Guillem 27 Feb '23

27 Feb '23

Hello all, I'm using modeller to mutate a single residue in a PDB template that contains ZN atoms. The mutation is taking place correctly, but the resulting PDB is written with the name ZN instead of ZN2, which is in the original template. My ZN is in a different coordination state and I need the name to stay ZN2 in the mutated structure. I have tried setting env.io.heatatm = True, but the outcome is the same. Is there a way to explicitly set modeller to leave the atom names untouched? Thanks in advance for any help. Pedro Here is my code: env = environ() env.io.atom_files_directory = ['.', './atom_files'] env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') env.io.hetatm = True #Prepare Modeller mdl = model(self.env, file=pdb_file) aln = alignment(self.env) aln.append_model(mdl, atom_files=pdb_file, align_codes=pdb_file) chain_id, res_id = mutatnt.split(":") pointmut = f'{res_id}:{chain_id}' new_residue = "A" sel = selection(mdl.residues[pointmut]) sel.mutate(residue_type=self.res1to3[new_residue]) #mutate # Generate the mutated model aln.append_model(mdl, align_codes='mut') mdl.clear_topology() mdl.generate_topology(aln['mut']) mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl2 = model(self.env, file=pdb_file) mdl.res_num_from(mdl2,aln) # Write the mutated structure to a PDB file mdl.write(file=output_file, model_format='PDB')

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Question on select_atoms vs. select_loop_atoms
by Wiley, Brian 12 Feb '23

12 Feb '23

Hi, When I write a new class that extends either AutoModel or AllHModel and I define the select_atoms() function only the atoms in those residues are modeled and the rest remain at their start position. However when extending LoopModel and write the same selection for select_loop_atoms(), all the atoms move. Is this intended by design? Brian Wiley Bioinformatics Scientist / Learner Washington University in St. Louis p. 480-370-4230 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 1

No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found
by Irawati Roy 10 Feb '23

10 Feb '23

Hello I am trying to build a model of a protein sequence where I have structure of two domains of the protein as an input. One structure is collected from PDB. another is simulation generated. I got the following error: Traceback (most recent call last): File "align1.py", line 7, in <module> mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:A')) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 101, in __init__ self.read(**vars) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 151, in read return _modeller.mod_model_read2(self.modpt, io.modpt, _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " FIRST", chain " A"; atom file name: A1.pdb The simulation generated structure file looks like following: ATOM 1 N MET X 1 43.720 45.860 63.480 0.00 0.00 ATOM 2 H1 MET X 1 44.460 45.570 64.150 0.00 0.00 ATOM 3 H2 MET X 1 42.750 45.730 63.840 0.00 0.00 ATOM 4 H3 MET X 1 43.890 45.180 62.720 0.00 0.00 ATOM 5 CA MET X 1 43.900 47.280 63.110 0.00 0.00 ATOM 6 HA MET X 1 43.520 47.850 63.950 0.00 0.00 ATOM 7 CB MET X 1 45.340 47.790 62.980 0.00 0.00 ATOM 8 HB1 MET X 1 45.450 48.870 62.740 0.00 0.00 The code used is the following: from modeller import * env = environ() aln = alignment(env) env.io.hetatm = True for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X')) aln.append_model(mdl, atom_files=pdb, align_codes=pdb) aln.append(file='query1.ali', align_codes='query') aln.malign() aln.write(file='querytemplate_new.ali', alignment_format='PIR') aln.write(file='querytemplate_new.pap', alignment_format='PAP') Any help regarding how to solve this error will be great. Thanks Ira

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Error: No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT
by irawatiroy＠gmail.com 10 Feb '23

10 Feb '23

Dear Users Hello I am trying to build a model of a protein sequence where I have structures of two domains of the same protein as an input. One structure is collected from PDB. another is simulation generated. I got the following error: Traceback (most recent call last): File "align1.py", line 7, in <module> mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:A')) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 101, in __init__ self.read(**vars) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 151, in read return _modeller.mod_model_read2(self.modpt, io.modpt, _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " FIRST", chain " A"; atom file name: A1.pdb The simulation generated structure file looks like following: ATOM 1 N MET X 1 43.720 45.860 63.480 0.00 0.00 ATOM 2 H1 MET X 1 44.460 45.570 64.150 0.00 0.00 ATOM 3 H2 MET X 1 42.750 45.730 63.840 0.00 0.00 ATOM 4 H3 MET X 1 43.890 45.180 62.720 0.00 0.00 ATOM 5 CA MET X 1 43.900 47.280 63.110 0.00 0.00 ATOM 6 HA MET X 1 43.520 47.850 63.950 0.00 0.00 ATOM 7 CB MET X 1 45.340 47.790 62.980 0.00 0.00 ATOM 8 HB1 MET X 1 45.450 48.870 62.740 0.00 0.00 ATOM 9 HB2 MET X 1 45.800 47.630 63.980 0.00 0.00 ATOM 10 CG MET X 1 46.250 47.060 61.990 0.00 0.00 ATOM 11 HG1 MET X 1 47.240 47.350 62.410 0.00 0.00 ATOM 12 HG2 MET X 1 46.180 45.950 62.040 0.00 0.00 ATOM 13 SD MET X 1 46.260 47.620 60.260 0.00 0.00 ATOM 14 CE MET X 1 47.960 47.000 60.080 0.00 0.00 ATOM 15 HE1 MET X 1 47.960 45.900 60.270 0.00 0.00 ATOM 16 HE2 MET X 1 48.350 47.180 59.060 0.00 0.00 ATOM 17 HE3 MET X 1 48.640 47.540 60.770 0.00 0.00 ATOM 18 C MET X 1 43.020 47.620 61.960 0.00 0.00 ATOM 19 O MET X 1 42.650 46.780 61.140 0.00 0.00 ATOM 20 N ALA X 2 42.710 48.920 61.800 0.00 0.00 ATOM 21 HN ALA X 2 43.190 49.580 62.370 0.00 0.00 ATOM 22 CA ALA X 2 42.060 49.460 60.650 0.00 0.00 ATOM 23 HA ALA X 2 41.530 48.650 60.160 0.00 0.00 ATOM 24 CB ALA X 2 41.310 50.730 61.090 0.00 0.00 ATOM 25 HB1 ALA X 2 41.940 51.410 61.700 0.00 0.00 The code used is the following: from modeller import * env = environ() aln = alignment(env) env.io.hetatm = True for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X')) aln.append_model(mdl, atom_files=pdb, align_codes=pdb) aln.append(file='query1.ali', align_codes='query') aln.malign() aln.write(file='querytemplate_new.ali', alignment_format='PIR') aln.write(file='querytemplate_new.pap', alignment_format='PAP') Any help regarding how to solve this error will be great. Thanks Ira

1 0

Generating chimeric protein from templates
by Ta-Chou Huang 06 Feb '23

06 Feb '23

Dear Users, I would like to generate a chimeric protein from templates, especially following the tips from FAQ 1 ( https://salilab.org/modeller/9.10/manual/node36.html) and also here https://salilab.org/modeller/9.10/manual/node21.html. To better understand the code and its meaning, I used two simple sequences together as test case. In pir file, it has: >P1;2xkmA structureN:2xkm GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA -------------------------------------------* >P1;4xknE structureX:4xkh ---------------------------------------------- NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE* >P1;test sequence:test GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE* and almost the same for ali file. However, using the build_profile.py, it shows the first error: _modeller.FileFormatError: parse_pir__E> Invalid PIR file header line: structureN:2xkm There should be 10 fields separated by colons, : This line actually contains 2 fields. Now here comes my question, from the FAQ, I thought it was enough to use two fields for the template? Even when I put enough colon to make it as 10 fields, it shows the next error that it could not find the PDB file. To fix this problem, I tried to put the entire information of the structureN (and structureX) line from the pdb_95.pir which I download from the Modeller website, with the same build_profile.py, the third error comes: _modeller.StatisticsError: regress_657E> Not enough bins in histogram - cannot calculate statistics, nbins: 1 In the end, I don't understand the exact problem to cause all these errors, did miss something in the pir or ali file? or I used the wrong script. Hope to hear any suggestions from you. Best wishes.

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modeller_usage